Complete chloroplast genome sequence of Fagopyrum dibotrys: genome features, comparative analysis and phylogenetic relationships

• Published in: Scientific reports Vol. 8; no. 1; pp. 12379 - 12
• Main Authors: Wang, Xumei, Zhou, Tao, Bai, Guoqing, Zhao, Yuemei
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 17.08.2018; Nature Publishing Group
• Subjects: 45/22; 631/181/757; 631/208/212/748; 631/208/721; Chloroplasts; Comparative analysis; Fagopyrum; Gene order; Genes; Genetics; Genomes; Humanities and Social Sciences; Inverted repeat; Medicinal plants; multidisciplinary; Nucleotide sequence; Phylogenetics; Phylogeny; Polygonaceae; Population genetics; Positive selection; Proteins; rRNA; Science; Science (multidisciplinary); Simple sequence repeats; tRNA; Wild plants
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-018-30398-6

Fagopyrum dibotrys , belongs to Polygonaceae family, is one of national key conserved wild plants of China with important medicinal and economic values. Here, the complete chloroplast (cp) genome sequence of F. dibotrys is reported. The cp genome size is 159,919 bp with a typical quadripartite structure and consisting of a pair of inverted repeat regions (30,738 bp) separated by large single copy region (85,134 bp) and small single copy region (13,309 bp). Sequencing analyses indicated that the cp genome encodes 131 genes, including 80 protein-coding genes, 28 tRNA genes and 4 rRNA genes. The genome structure, gene order and codon usage are typical of angiosperm cp genomes. We also identified 48 simple sequence repeats (SSR) loci, fewer of them are distributed in the protein-coding sequences compared to the noncoding regions. Comparison of F. dibotrys cp genome to other Polygonaceae cp genomes indicated the inverted repeats (IRs) and coding regions were more conserved than single copy and noncoding regions, and several variation hotspots were detected. Coding gene sequence divergence analyses indicated that five genes ( ndhK, petL rpoC2, ycf1, ycf2 ) were subject to positive selection. Phylogenetic analysis among 42 species based on cp genomes and 50 protein-coding genes indicated a close relationship between F. dibotrys and F. tataricum . In summary, the complete cp genome sequence of F. dibotrys reported in this study will provide useful plastid genomic resources for population genetics and pave the way for resolving phylogenetic relationships of order Caryophyllales.